Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce

Abstract

Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.

Keywords: Norway spruce; candidate genes; functional trait mapping; genome-wide association mapping; sequence capture; single nucleotide polymorphisms.

Figure 1

EBV trajectories of four wood quality traits over time: (a) wood density, (b) late wood density, (c) annual ring width and (d) late wood ring width. Individual trajectories for each trait are shown in light blue lines and the black line represents the mean trajectory for the phenotype. These trajectories were used to determine the four latent traits of each tree, using linear splines with two knots.

Figure 2

(a) Decay of linkage disequilibrium (LD) across all the tagged genomic sequences, the majority being exonic regions. The squared correlation coefficient between loci (r²) is plotted against distance, in base pairs, separating loci. The fitted curve (red) is representative of the trend of decay from the 178 101 SNPs utilized in the association mapping (AM). (b) Decay of LD with distance in base pairs between sites from across 41 contigs with significant associations. (c) Decay of LD across contig MA_96191 that has a significant association for ratio of percentage earlywood vs latewood on which two probes were captured. (d) Decay of LD on contig MA_80033 indicating the variable LD in the genome.

Figure 3

Box plot of the estimated genotypic effect on the phenotypes in the study. The significant SNPs associated and each one of the traits have been correlated to give the impact each genotype has on the average of the overall trait

Figure 4

The heatmap showing the expression levels (VST values) of spruce candidate genes in different organs and tissues based on data of Nystedt et al. (2013) available at http://congenie.org.